Ana G. Cobián-Güemes
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View article: Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates Open
Resistance to antibiotics is approaching crisis levels for organisms such as the ESKAPEE pathogens (includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter …
View article: Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States
Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States Open
The resurgence of phage therapy in Western societies has been in direct response to recent increases in antimicrobial resistance (AMR) that have ravaged many societies. While phage therapy as a concept has been around for over 100 years, i…
View article: Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data
Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data Open
Motivation Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identif…
View article: <i>In vitro</i> resensitization of multidrug-resistant clinical isolates of <i>Enterococcus faecium</i> and <i>E. faecalis</i> through phage-antibiotic synergy
<i>In vitro</i> resensitization of multidrug-resistant clinical isolates of <i>Enterococcus faecium</i> and <i>E. faecalis</i> through phage-antibiotic synergy Open
Bacteriophages are an increasingly attractive option for the treatment of antibiotic-resistant infections, but their efficacy is difficult to discern due to the confounding effects of antibiotics. Phages are generally delivered in conjunct…
View article: Experimental Phage Evolution Results in Expanded Host Ranges Against MDR and XDR<i>Klebsiella pneumoniae</i>Isolates
Experimental Phage Evolution Results in Expanded Host Ranges Against MDR and XDR<i>Klebsiella pneumoniae</i>Isolates Open
Resistance to antibiotics is approaching crisis levels for organisms such as the ESKAPEE pathogens (includes Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , Pseudomonas aeruginosa , Enteroba…
View article: Phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data
Phage therapy candidates from Sphae: An automated toolkit for predicting sequencing data Open
Motivation Phage therapy is a viable alternative for treating bacterial infections amidst the escalating threat of antimicrobial resistance. However, the therapeutic success of phage therapy depends on selecting safe and effective phage ca…
View article: Identification of a large cohort of Enterobacter jumbo phages with broad host ranges across pathogenic Gammaproteobacteria
Identification of a large cohort of Enterobacter jumbo phages with broad host ranges across pathogenic Gammaproteobacteria Open
ESKAPE pathogens cause most hospital-acquired infections globally and often carry antibiotic resistance. Many of them have been the target of bacteriophage therapies. Enterobacter is an ESKAPE pathogen but is less frequently a target for p…
View article: <i>In-vitro</i>resensitization of multidrug resistant clinical isolates of<i>Enterococcus faecium</i>and<i>faecalis</i>through phage-antibiotic synergy
<i>In-vitro</i>resensitization of multidrug resistant clinical isolates of<i>Enterococcus faecium</i>and<i>faecalis</i>through phage-antibiotic synergy Open
Bacteriophages are an increasingly attractive option for the treatment of antibiotic resistant infections, but their efficacy is difficult to discern due to confounding effects of antibiotics. Phages are generally delivered in conjunction …
View article: A simple solid media assay for detection of synergy between bacteriophages and antibiotics
A simple solid media assay for detection of synergy between bacteriophages and antibiotics Open
The emergence of antibiotic-resistant bacteria (ARB) has necessitated the development of alternative therapies to deal with this global threat. Bacteriophages (viruses that target bacteria) that kill ARB are one such alternative. Although …
View article: Jumbo phages are active against extensively drug-resistant eyedrop-associated <i>Pseudomonas aeruginosa</i> infections
Jumbo phages are active against extensively drug-resistant eyedrop-associated <i>Pseudomonas aeruginosa</i> infections Open
Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria …
View article: A simple solid media assay for detection of synergy between bacteriophages and antibiotics
A simple solid media assay for detection of synergy between bacteriophages and antibiotics Open
The emergence of antibiotic resistant bacteria (ARB) has necessitated the development of alternative therapies to deal with this global threat. Bacteriophages (viruses that target bacteria) that kill ARB are one such alternative. While pha…
View article: Compounding Achromobacter Phages for Therapeutic Applications
Compounding Achromobacter Phages for Therapeutic Applications Open
Achromobacter species colonization of Cystic Fibrosis respiratory airways is an increasing concern. Two adult patients with Cystic Fibrosis colonized by Achromobacter xylosoxidans CF418 or Achromobacter ruhlandii CF116 experienced fatal ex…
View article: Jumbo phages are active against extensively-drug-resistant eyedrop-associated<i>Pseudomonas aeruginosa</i>infections
Jumbo phages are active against extensively-drug-resistant eyedrop-associated<i>Pseudomonas aeruginosa</i>infections Open
Antibiotic resistant bacteria present an emerging challenge to human health as the pressure instituted on the microbial world through the liberal use of antibiotics has resulted in their emergence across the globe. Those bacteria that acqu…
View article: Microbiome of Sri Lankan Coral Reefs: An Indian Ocean Island Subjected to a Gradient of Natural and Anthropogenic Impacts
Microbiome of Sri Lankan Coral Reefs: An Indian Ocean Island Subjected to a Gradient of Natural and Anthropogenic Impacts Open
Coral reefs around Sri Lanka have coexisted with human communities for thousands of years and are a continual source of food, economic productivity, and tourism. Although these reef systems sustain nearby populations, little is known about…
View article: Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis
Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis Open
View article: Correction for Merenstein et al., “Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome”
Correction for Merenstein et al., “Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome” Open
Volume 12, no. 4, e01777-21. https://doi.org/10.1128/mBio.01777-21. In Table S5 in the supplemental material, two primer sequences were listed incorrectly. The actual sequence of TTV_3656_Fwd is AGACTCCGAGDTGCYMTTGG, and the actual sequenc…
View article: Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome
Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome Open
Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF…
View article: Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome
Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome Open
COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understoo…
View article: Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs
Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs Open
To control community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the 2020 global pandemic, most countries implemented strategies based on direct human testing, face covering, and surface disinfection…
View article: Signatures of COVID-19 severity and immune response in the respiratory tract microbiome
Signatures of COVID-19 severity and immune response in the respiratory tract microbiome Open
Rationale Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Objective To define the respiratory tract microbiome in COVID-19 …
View article: A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes Open
To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture me…
View article: A multiomic analysis of in situ coral–turf algal interactions
A multiomic analysis of in situ coral–turf algal interactions Open
Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components o…
View article: Multi-omics study of keystone species in the cystic fibrosis lung microbiome
Multi-omics study of keystone species in the cystic fibrosis lung microbiome Open
Background: Ecological networking and in vitro studies have predicted that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes by sustaining the growth of canonical CF pathogens. Here, a multi-omics…
View article: A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes
A Distinct Contractile Injection System Found in a Majority of Adult Human Microbiomes Open
An imbalance of normal bacterial groups such as Bacteroidales within the human gut is correlated with diseases like obesity. A current grand challenge in the microbiome field is to identify factors produced by normal microbiome bacteria th…
View article: Efficient whole genome sequencing of influenza A viruses
Efficient whole genome sequencing of influenza A viruses Open
The constant threat of emergence for novel pathogenic influenza A viruses with pandemic potential, makes full-genome characterization of circulating influenza viral strains a high priority, allowing detection of novel and re-assorting vari…
View article: A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage Open
View article: Additional file 10: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Additional file 10: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage Open
Annotation of the VR-containing ORFs in DGRs. All ORFs with a VR were annotated using Phyre2 and HMM searches against the Pfam-A database. Annotations were only considered significant if the Phyre2 confidence is > 97 or HMMer bitscore is >…
View article: Additional file 8: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Additional file 8: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage Open
Fractional abundance of Hankyphage in viromes. The Hankyphage genome was used as a reference to align reads from each human virome at 97% identity. For each virome containing > 1 aligned read (n = 221), the fractional abundance of Hankypha…
View article: Additional file 2: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Additional file 2: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage Open
Nucleotide coordinates, taxonomy, and coverage of the DGR cassettes. The nucleotide coordinates of the reverse transcriptase, template repeat and variable repeat on the predicted prophage-containing region are listed in columns A–H (only t…
View article: Additional file 4: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Additional file 4: of A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage Open
Proportion of temperate and lytic viruses in the phage databases (RefSeq, PhagesDB, and DGR-containing prophage collection). Each phage life history was classified using PHACTS as ‘lytic’ or ‘temperate’ if the trees voting for that lifesty…